Protecting groups and associated deprotection methods are widely used in organic synthesis. See, e.g., Greene et al., Protective Groups in Organic Synthesis, 3rd Ed., John Wiley & Sons, Inc., New York, N.Y. (1999). Protecting groups are often used to prevent a particular functional group or part of a molecule (e.g., an amine, a carboxylic acid, a hydroxyl, a heterocycle, etc.) from reacting under certain reaction conditions (e.g., a chemical reaction in which an unprotected part of the same molecule undergoes a synthetic transformation). Hydroxyl-protecting groups are among the most commonly used protecting groups and are of great importance in organic synthesis. Hydroxyl-protecting groups are particularly useful in the synthesis of oligonucleotides, which are the subject of extensive research and development efforts in view of their significant potential therapeutic applications.
The therapeutic application of oligonucleotides is based on the selective formation of hybrids between antisense oligonucleotides and complementary nucleic acids, such as messenger RNAs (mRNAs). Such hybrids inhibit gene expression by preventing the translation of mRNAs into proteins. Nuclease-resistant oligonucleotides, such as thioated oligonucleotides, are highly desirable in this regard. The discovery and development of improved methods for synthesizing nuclease-resistant oligonucleotides continue to be important goals in medicinal chemistry research.
The method most commonly used for the synthesis of thioated oligonucleotides is the phosphoramidite method with stepwise sulfurization (see, e.g., U.S. Pat. Nos. 4,415,732; 4,668,777; 4,973,679; 4,845,205; and 5,525,719). Alternatively, oligonucleotides can be synthesized using an N-acylphosphoramidite method with stepwise sulfurization (see International Patent Application Publication No. WO 00/56749). In such methods, each coupling step typically is performed with a hydroxyl-protected nucleoside phosphoramidite or N-acylphosphoramidite (e.g., a nucleoside or oligonucleotide phosphoramidite or N-acylphosphoramidite bearing a 5′- or a 3′-hydroxyl protecting group). After each nucleotide addition cycle, the terminal hydroxyl-protecting group is removed so that the next coupling step can be carried out in succession. Acid-labile hydroxyl-protecting groups in oligonucleotide synthesis are known. Examples of acid-labile hydroxyl protecting groups are described in U.S. Pat. Nos. 4,415,732; 4,668,777; and 5,705,621. Such hydroxyl-protecting groups require acidic conditions for deprotection, which is particularly disadvantageous when the oligonucleotide is acid-labile or contains one or more acid-labile functional groups. Photolabile hydroxyl-protecting groups have been described, e.g., in U.S. Pat. Nos. 5,889,165 and 5,763,599. However, photolabile hydroxyl-protecting groups require photochemical conditions for their removal, which is particularly disadvantageous when the oligonucleotide is photosensitive or contains one or more photosensitive functional groups. Accordingly, the range of structural oligonucleotide analogs that can be prepared using conventional hydroxyl protection technology is often limited to those that are stable under such acidic and/or photochemical deprotection conditions.
Accordingly, there is a need for hydroxyl-protecting groups that can be removed under mild conditions, and for methods of using such protecting groups. The invention provides such protecting groups and methods. These and other objects and advantages of the invention, as well as additional inventive features, will be apparent from the description of the invention provided herein.